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AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. Augustus [gene prediction] University of Göttingen - Faculty of Biology - Institute of Microbiology and Genetics - Department of Bioinformatics
- Predictions
Augustus [predictions] Predictions for Chlamydomonas...
- References
Using native and syntenically mapped cDNA alignments to...
- Accuracy
AUGUSTUS is used in many genome annotation projects. Below...
- Datasets
The following sequence files were used to train AUGUSTUS or...
- Department of Bioinformatics
Follow Göttingen Bioinformatics on Twitter: Follow...
- Mario Stanke
"AUGUSTUS: a web server for gene finding in eukaryotes",...
- Augustus Incorporating Rna-Seq
The general approach is to generate hints for Augustus from...
- Help
But AUGUSTUS predicts at least one gene (if possible)....
- Predictions
Augustus is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server, on a new web server for larger input files or be downloaded and run locally. It can incorporate data from RNA-Seq, protein homology, ESTs, conservation and other sources of information.
- Mario Stanke
- 2003
- Gene Prediction with AUGUSTUS
- INTRODUCTION
- Windows
- Ubuntu 18.04, Debian 9 or later
- Docker
- Singularity
- Building AUGUSTUS from source
- WEB-SERVER
- REFERENCES AND DOCUMENTATION
- LICENSES
AUGUSTUS is a program to find genes and their structures in one or more genomes. More ...
Windows users can use the Windows Subsystem for Linux (WSL) to install AUGUSTUS exactly as described below for Linux. How to set up the WSL for AUGUSTUS is described here.
Until Ubuntu 21.04 and Debian 11 only as single-genome version, since then with capability for comparative gene prediction.
Create a docker image from Dockerfile using:
Create a Singularity Image File from the Singularity Definition File using
Install locally
As a normal user, add the directory of the executables to the PATH environment variable, for example:
Install globally
You can install AUGUSTUS globally, if you have root privileges, for example: Alternatively, you can exectue similar commands to those in the "install" section of the top-level Makefile to customize the global installation.
Optional: set environment variable AUGUSTUS_CONFIG_PATH
If the environment variable AUGUSTUS_CONFIG_PATH is set, augustus and etraining will look there for the config directory that contains the configuration and parameter files, e.g. '~/augustus/config'. You may want to add this line to a startup script (like ~/.bashrc). If this environment variable is not set, then the programs will look in the path ../config relative to the directory in which the executable lies. As a third alternative, you can specify this directory on the command line when you run augustus: --AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/
AUGUSTUS can also be run through a web-interface at http://bioinf.uni-greifswald.de/augustus/ and a web service at http://bioinf.uni-greifswald.de/webaugustus/.
Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24(5), pages 637–644, doi: 10.1093/bioinformatics/btn013
For further references see docs/REFERENCES.md
All source code, i.e.
•the AUGUSTUS source code (src/*.cc, include/*.hh)
•the scripts (scripts/*)
•the auxiliary programs (auxprogs/)
•the tree-parser (src/scanner, src/parser)
•the unit tests (src/unittests)
WebAUGUSTUS is a web server that allows you to predict genes in eukaryotic genomic sequences and train AUGUSTUS for novel species. AUGUSTUS is a program that usually produces accurate gene predictions for the species it is trained for.
- Katharina J. Hoff
- 2011
AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence.
Jul 1, 2004 · AUGUSTUS—A NEW APPROACH TO HMM-BASED GENE PREDICTION. AUGUSTUS is based on a generalized Hidden Markov Model (GHMM). This model defines probability distributions for the various sections of genomic sequences.
AUGUSTUS is a gene prediction program written or maintained by Mario Stanke, Oliver Keller, Stefanie König, Lizzy Gerischer, Katharina Hoff, Giovanna Migliorelli, Lars Gabriel, Anica Hoppe, Tonatiuh Peña Centeno, Henry Mehlan, Daniel Honsel and Steffen Herbold.
